Shito! Kyofu no kokushiken - S1-E11
Plot hole: Changes made in the anime only make nonsensical the mechanics of the fight against Black Pegasus. The villain focuses on dealing one big hit to the side of the hero at the cost of his life, but that big hit happens just in the anime and has no consequence or purpose at all. Seiya collapses later with various black spots from the hits of the first barrage, the one that he thought gave him no damage and went instead under the armor, just like in the manga. Black Pegasus had already dealt his death blow by that time, and what he does in the anime in addition to that has no consequence or meaning.
Taose! Ankoku Phoenix gundan - S1-E8
Plot hole: Andromeda is wearing his full armor (he's the only one doing that) at the end of the episode. The armor includes the chain that is used three times just in this episode alone to detect the bad guys, and that does it without need for explicit orders to do so, but with no explanation he's not detecting the enemy behind the tree. (00:22:10)
Fenikkusu! Jigoku o mita senshi - S1-E6
Plot hole: Shiryu tells Seiya that he had a feeling that someone was watching them from the shadows "ever since our fight ended." That makes no sense, since he was comatose (and he says himself that Shunrei had to tell him what happened). In the manga, he says that he had this feeling since the tournament began, which makes much more sense (plus Phoenix does not show up at that specific time being detected by the Andromeda chain). (00:03:35)
Kiseki no fukkatsu! Yuyo no cosmo - S1-E5
Plot hole: Miho is watching the match at home, and it is day - the kids in the previous episode also entered the Dome when it was afternoon, and a clock at their place when they watched the first of Seiya's fights showed it was 4 pm. Yet she takes a taxi for the arena when it's dark outside.
Cygnus! Hyogen no senshi - S1-E3
Plot hole: The tide of the fight turns when Hyoga revealed that he was never affected by Hydra's poison because nothing can break the defenses of his Cloth. But the claws DO make huge holes, that are then nowhere to be seen by the end of the episode, and yet, a plot point from later in the series, Cloths do not have self repairing abilities - not at that time of the series at least.
Cygnus! Hyogen no senshi - S1-E3
Plot hole: Saori Kido's presentation does not make a lick of sense. Assuming it happens through some odd holographic mechanism never seen before or after, it's day 3 of the tournament, so it appears extravagant that only then she'd start telling the audience what the Galaxian Wars are. Second.it's day 3 of the tournament.and the third match. That means that they have been packing a stadium with dozens of thousands of people, who come over for ONE match that lasts a few minutes. That's a real stretch, to say the least. There's also a minor but kinda funny matter; the way the cameras are shown pointing, the whole world is tuned into an uninterrupted upskirt shot of Saori Kido delivering her solemn speech.